Academic literature on the topic 'GWAS replication'

Alzheimer’s disease (AD) is the most common neurodegenerative disorder. Using discrete disease status as the phenotype and computing statistics at the single marker level may not be able to address the underlying biological interactions that contribute to disease mechanism and may contribute to the issue of “missing heritability.” We performed a genome-wide association study (GWAS) and a genome-wide interaction study (GWIS) of an amyloid imaging phenotype, using the data from Alzheimer’s Disease Neuroimaging Initiative. We investigated the genetic main effects and interaction effects on cingulate amyloid-beta (Aβ) load in an effort to better understand the genetic etiology of Aβdeposition that is a widely studied AD biomarker. PLINK was used in the single marker GWAS, and INTERSNP was used to perform the two-marker GWIS, focusing only on SNPs withp≤0.01for the GWAS analysis. Age, sex, and diagnosis were used as covariates in both analyses. Correctedpvalues using the Bonferroni method were reported. The GWAS analysis revealed significant hits within or proximal toAPOE,APOC1, andTOMM40genes, which were previously implicated in AD. The GWIS analysis yielded 8 novel SNP-SNP interaction findings that warrant replication and further investigation.

AimsOsteoporosis (OP) is a metabolic bone disease, characterized by a decrease in bone mineral density (BMD). However, the research of regulatory variants has been limited for BMD. In this study, we aimed to explore novel regulatory genetic variants associated with BMD.MethodsWe conducted an integrative analysis of BMD genome-wide association study (GWAS) and regulatory single nucleotide polymorphism (rSNP) annotation information. Firstly, the discovery GWAS dataset and replication GWAS dataset were integrated with rSNP annotation database to obtain BMD associated SNP regulatory elements and SNP regulatory element-target gene (E-G) pairs, respectively. Then, the common genes were further subjected to HumanNet v2 to explore the biological effects.ResultsThrough discovery and replication integrative analysis for BMD GWAS and rSNP annotation database, we identified 36 common BMD-associated genes for BMD irrespective of regulatory elements, such as FAM3C (pdiscovery GWAS = 1.21 × 10-25, preplication GWAS = 1.80 × 10-12), CCDC170 (pdiscovery GWAS = 1.23 × 10-11, preplication GWAS = 3.22 × 10-9), and SOX6 (pdiscovery GWAS = 4.41 × 10-15, preplication GWAS = 6.57 × 10-14). Then, for the 36 common target genes, multiple gene ontology (GO) terms were detected for BMD such as positive regulation of cartilage development (p = 9.27 × 10-3) and positive regulation of chondrocyte differentiation (p = 9.27 × 10-3).ConclusionWe explored the potential roles of rSNP in the genetic mechanisms of BMD and identified multiple candidate genes. Our study results support the implication of regulatory genetic variants in the development of OP.Cite this article: Bone Joint Res 2023;12(2):147–154.

In genome-wide association study (GWAS), robust genetic association tests such as maximum of three CATTs (MAX3), each corresponding to recessive, additive, and dominant genetic models, the minimumpvalue of Pearson’s Chi-square test with 2 degrees of freedom, and CATT based on additive genetic model (MIN2), genetic model selection (GMS), and genetic model exclusion (GME) methods have been shown to provide better power performance under wide range of underlying genetic models. In this paper, we demonstrate how these robust tests can be applied to the replication study of GWAS and how the overall statistical significance can be evaluated using the combined test formed bypvalues of the discovery and replication studies.

Genome-wide association studies [GWAS] have identified a limited number of endometrial cancer risk loci by analyzing single nucleotide polymorphisms [SNPs]. We hypothesized that analyzing haplotypes rather than SNPs could provide novel and more detailed information on genetic cancer susceptibility loci. To examine the association of a SNP or haplotype with endometrial cancer risk we performed a two-stage haplotype GWAS. The discovery GWAS included a sub-cohort of 1,116 Swedish endometrial cancer cases and 5,021 controls from previously published GWAS data. A sliding window analysis was employed with window sizes of 1-25 SNPs using a logistic regression model. The Swedish haplotype analysis identified 15 novel candidate risk loci (2q31.1, 4p16.1, 4p15.31, 6q13, 7p21.1, 9p13.3, 10q26.3, 11q21, 12q13.11, 13q12.11, 15q13.3, 16q24.3, 19q13.32, 20p12.3 and 22q13.2) with OR ranging from 1.6 to 3.3 and p-values from 4.25 × 10−8 to 9.86 × 10−15. A second replication haplotype analysis of the Swedish novel loci was performed using two cohorts from Belgium and Germany. In spite of small sample sizes in the replication cohorts, there was still support for most loci with positive ORs. In addition, the findings in the two European cohorts motivates further studies to search for founder haplotypes. These novel findings suggested that endometrial cancer loci, identified through haplotype analysis, conferred a higher risk compared to previous single-variant GWAS.

ObjectivesTo perform a genome-wide association study (GWAS) of gout cases versus asymptomatic hyperuricaemia (AH) controls, and gout cases versus normouricaemia controls, and to generate a polygenic risk score (PRS) to determine gout-case versus AH-control status.MethodsGout cases and AH controls (serum urate (SU) ≥6.0 mg/dL) from the UK Biobank were divided into discovery (4934 cases, 56 948 controls) and replication (2115 cases, 24 406 controls) cohorts. GWAS was conducted and PRS generated using summary statistics in discovery cohort as the base dataset and the replication cohort as the target dataset. The predictive ability of the model was evaluated. GWAS were performed to identify variants associated with gout compared with normouricaemic controls using SU <6.0 mg/dL and <7.0 mg/dL thresholds, respectively.ResultsThirteen independent single nucleotide polymorphisms (SNPs) in ABCG2, SLC2A9, SLC22A11, GCKR, MEPE, PPM1K-DT, LOC105377323 and ADH1B reached genome-wide significance and replicated as predictors of AH to gout transition. Twelve of 13 associations were novel for this transition, and rs1229984 (ADH1B) was identified as GWAS locus for gout for the first time. The best PRS model was generated from association data of 17 SNPs; and had predictive ability of 58.5% that increased to 69.2% on including demographic factors. Two novel SNPs rs760077(MTX1) and rs3800307(PRSS16) achieved GWAS significance for association with gout compared with normouricaemic controls using both SU thresholds.ConclusionThe association of urate transporters with gout supports the central role of hyperuricaemia in its pathogenesis. Larger GWAS are required to identify if variants in inflammatory pathways contribute to progression from AH to gout.

Abstract Background Previous genome wide association studies (GWASs) have identified over 200 susceptibility loci for inflammatory bowel diseases (IBD), but studies in non-European population are limited. To clarify the genetic background of ulcerative colitis (UC) in the Japanese population, we conducted GWAS using a population specific SNP array (Japonica Array). Methods Discovery GWAS included 624 UC patients and 2004 healthy controls (HC) and replication study included 1075 UC patients and 419 HCs. We performed GWAS using a Japonica Array and the subsequent imputation with a Japanese population reference panel (referred to as 2KJPN). After GWAS, significant and candidate loci were identified and the representative top SNPs of each region were analysed in replication study and combined analysis. The probability of colectomy between genotypes of rs117506082, the top hit SNP at HLA loci, was analysed using the Kaplan–Meier method. Results In the GWAS, only the HLA loci showed genome wide significant association [rs117506082, p = 6.69E−28, OR=1.29, 95%CI=1.23–1.35]. 7 regions with nominal significance included 2 known loci: IL23R [rs76418789, p = 6.29E−7, OR=0.89, 95%CI=0.85–0.93], IRF8 [rs16940202, p = 1.03E−6, OR=1.07, 95%CI=1.04–1.10] and 5 novel loci: miR-622 [rs9560575, p = 8.23E−7, OR=1.06, 95%CI=1.04–1.09], 14q31 [rs117618617, p = 1.53E−6, OR=1.13, 95%CI=1.09–1.19], KAT6B [rs12260609, p = 1.81E−6, OR=1.06, 95%CI=1.04–1.09], PAX3-CCDC140-SGPP2 [rs7589797, p = 2.87E−6, OR=0.94, 95%CI=0.93–0.97], KCNA2 [rs118020656, p = 4.01E−6, OR=1.12, 95%CI=1.07–1.18]. Combined analysis revealed that the HLA loci [rs117506082, p = 1.10E−23, OR=3.43, 95%CI=2.99–3.83] and IL23R p.G149R [rs76418789, p = 9.03E−11, OR=0.51, 95%CI=0.42–0.63] had a genome wide significant association. The GG genotype of rs117506082 had a significantly lower probability for total colectomy compared with the GA+AA genotype (p = 1.72E−2). Conclusion IL23R p.G149R is a susceptibility locus for UC in Japanese individuals. The GG genotype of rs117506082 at HLA loci, a risk genotype for UC susceptibility, may predict a better clinical course.

The present study aimed to summarize and validate the genomic association signals for diabetic retinopathy (DR), proliferative DR, and diabetic macular edema/diabetic maculopathy. A systematic search of the genome-wide association study (GWAS) catalog and PubMed/MELINE databases was conducted to curate a comprehensive list of significant GWAS discoveries. The top signals were then subjected to meta-analysis using established protocols. The results indicate the need for improved consensus among DR GWASs, highlighting the importance of validation efforts. A subsequent meta-analysis confirmed the association of two SNPs, rs4462262 (ZWINT-MRPS35P3) (odds ratio = 1.38, p = 0.001) and rs7903146 (TCF7L2) (odd ratio = 1.30, p < 0.001), with DR in independent populations, strengthening the evidence of their true association. We also compiled a list of candidate SNPs for further validation. This study highlights the importance of consistent validation and replication efforts in the field of DR genetics. The two identified gene loci warrant further functional investigation to understand their role in DR pathogenesis.

La lèpre, maladie infectieuse chronique causée par Mycobacterium leprae, affecte principalement la peau, les nerfs et les yeux avec des séquelles majeures en l’absence de traitement. Avec 200 000 nouveaux cas diagnostiqués chaque année (1 toutes les 2 minutes), il s’agit de la mycobactériose la plus commune après la tuberculose et requalifiée « maladie tropicale négligée » en 2017 par l’Organisation Mondiale de la Santé (OMS). Si la contribution génétique de l’hôte dans l’histoire naturelle de la maladie est maintenant bien établie, son architecture reste lacunaire. Dans cette continuité et afin de la préciser, nous avons, pour la première fois, utilisé une approche de génétique épidémiologique familiale. Plus précisément, nous avons réalisé la première étude d’association pangénomique (Genome-Wide Association Study, GWAS) familiale sur la lèpre. Ainsi, au cours des 20 dernières années, un échantillon de 481 familles nucléaires, parents et enfants, sélectionnées à partir d’un enfant atteint, a été constitué au Vietnam. Sur cet échantillon primaire de 1749 individus incluant 622 enfants atteints, nous avons testé l’association de près de 6 millions de variants bi-alléliques (Single Nucleotide Polymorphism, SNP), génotypés ou imputés, avec la lèpre. Dans un second temps, nous avons testé les signaux les plus prometteurs dans un échantillon de réplication, c’est-à-dire, indépendant et issu de la même population, constitué de 1 181 cas et 668 contrôles. Les résultats les plus significatifs ont été observés au sein de la région HLA et l’analyse multivariée a permis d’identifier trois signaux indépendants. Deux dans la région HLA classe I : rs1265048 [Odds-ratio (OR) = 0,69 ; p-val = 5,5.10⁻¹¹] et rs114598080 [OR = 1,47 ; p-val = 8,8.10⁻¹³] ; Et un dans la région HLA classe II : rs3187964 [OR = 1,67 ; p-val = 8,4.10⁻¹⁶]. Nous avons également identifié deux signaux hors HLA : un variant faux-sens dans le gène LACC1 (rs3764147 : OR = 1,52 ; p-val = 5,1.10⁻¹⁴), et un variant à proximité du gène IL12B (rs6871626 : OR = 0,73 ; p-val = 6.4.10⁻⁸). Les contraintes de coûts des études pangénomiques imposent une réduction majeure du nombre de SNPs à tester dans d’autres échantillons. Dans les études familiales, les parents sont de fait génotypés et pourraient permettre une réplication immédiate sans coûts ajoutés. Au moyen d’une large étude de simulation, nous avons montré que cette approche était pertinente. Une étude cas-contrôle chez les parents de l’échantillon primaire est une réplication valide, statistiquement indépendante de l’étude d’association familiale. C’est un argument fort en faveur des approches familiales pour l’exploration pangénomique de la contribution génétique de l’hôte dans les phénotypes complexes. La compréhension de la physiopathologie de l'infection à M. leprae est cruciale pour optimiser les approches préventives selon les profils génétiques à plus haut risque, et ouvrir de nouvelles pistes thérapeutiques en précisant les cascades fonctionnelles pertinentes. En ce sens, la dissection du contrôle génétique de l'infection par l'hôte est indispensable. Enfin, remettre la famille au cœur de la quête génétique, c’est remettre la génétique dans son milieu naturel<br>Leprosy is a chronic infectious disease caused by Mycobacterium leprae. It primarily affects the skin and peripheral nerves, and can cause an irreversible impairment of nerve function, often leading to severe disabilities and social stigma if left untreated. The disease, re-qualified by WHO (World Health Organization) as a “Neglected Tropical Disease” in 2017, remains a major public health problem in regions of endemic countries, with over 200,000 new cases per year (one every two minutes). It is ranked second as the most common mycobacterial infectious disease, right after tuberculosis. While it has been well established that there is a genetic contribution to this disease, the underlying genetic causes remains unknown. In our study, we sought to reveal the host´s genetic architecture of leprosy by taking of a familial epidemiological approach. We conducted the first Family-Based Genome-Wide Association Study (GWAS) of leprosy in 481 Vietnamese nuclear families (parents and children) selected based on one affected child and collected over the past 20 years. Using this sample of 1,749 individuals, including 622 affected offspring, we performed association tests between six million biallelic genetic variants (Single-Nucleotide Polymorphism, genotyped or imputed) and the binary phenotype of disease status. Following this first analysis, we conducted a replication analysis of the most promising results in an independent sample of the same ethnic origin, accounting for 1,181 cases and 668 controls. The most significant results were observed within the HLA (Human Leukocyte Antigen) region, in which 3 independent SNPs displayed genome-wide significant associations. Among these, two were for the HLA class I region and one for the HLA class II (rs1265048 [OR = 0.69; p-value = 5.5x10⁻¹¹], rs114598080 [OR = 1.47; p-value = 8.8x10⁻¹³] and rs3187964 [OR = 1.67; p-value = 8.4x10⁻¹⁶] respectively). We also identified a missense variant in the LACC1 gene (rs3764147: OR = 1.52; p-value = 5.1x10⁻¹⁴) and an intergenic variant located close to the IL12B gene (rs6871626: OR = 0.73; p-value = 6.4x10⁻⁸). LACC1 encodes a central regulator of the metabolic function and bioenergetic state of macrophages and IL12B encodes IL-12p40, which is common to two interleukins, IL-12 and IL-23. Large GWAS are expensive, strongly limiting the number of variants to test in a replication set. Here, we took advantage of the available parental phenotypic and genotypic information to perform a classical case-control study among the parents of the family-based sample. Indeed, using of extensive computer simulations, we demonstrated that this population-based parental study is a valid, powerful and costless replication strategy to confirm family-based associations. Overall, our observations add to the attractiveness of family-based designs and should provide valuable help for investigators planning to perform GWA studies. Understanding leprosy pathophysiology infection is crucial to optimize preventive approaches based on genetic profiles. Dissection of the genetic control of the infection by M. leprae by its human host, therefore, constitutes an indispensable step. Finally, repositioning the family at the heart of the genetic quest means repositioning genetics into its natural environment

Abstract Early twin and family studies point to a significant genetic contribution to Tourette syndrome (TS). Informed by early segregation analyses in TS families pointing to a single-gene autosomal dominant inheritance pattern with partial penetrance, initial efforts at gene discovery in TS utilized parametric linkage analysis in large multigenerational families but failed to identify a single specific genetic locus. Later segregation analyses supported the current characterization of TS as a complex, genetically heterogeneous disorder. Nonparametric linkage analyses have yet to identify common TS risk alleles. Candidate gene association studies in TS have not yielded significant reproducible findings. Genome-wide association studies (GWAS) have proven valuable for identifying and replicating loci for common complex traits and disorders across the medical field. A GWAS meta-analysis of almost 5,000 cases identified a significant locus in FLT3. Polygenic risk scores, calculated from the most recent TS GWAS summary statistics, have shown correlation with tic severity and affected status in independent samples. There has been an increasing effort to evaluate the contribution of rare allele variants toward TS. Recent studies have found a greater burden of rare copy number variants in TS cases; the largest study to date identified NRXN1 and CNTN6 as TS risk genes. Identifying rare de novo single nucleotide variants and indels in more than 800 parent–child trios has so far identified six likely TS risk genes (WWC1, CELSR3, OPA1, NIPBL, FN1, and FBN2), which present an enriched function for cell polarity.

Research into the genetic predisposition to superior athletic performance has been a hindered by the underpowered studies and the small effect size of identified genetic variants. The aims of this study were to investigate the association of common single-nucleotide polymorphisms (SNPs) with endurance athlete status in a large cohort of elite European athletes using GWAS approach, followed by replication studies in Russian and Japanese elite athletes and functional validation using metabolomics analysis. Results: The association of 476,728 SNPs of Illumina DrugCore Gene chip and endurance athlete status was investigated in 796 European international-level athletes (645 males, 151 females) by comparing allelic frequencies between athletes specialized in sports with high (n=662) and low/moderate (n=134) aerobic component. Validation of results was performed by comparing the frequencies of the most significant SNPs between 242 and 168 elite Russian high and low/moderate aerobic athletes, respectively, and between 60 elite Japanese endurance athletes and 406 controls. A meta-analysis has identified rs1052373 (GG homozygotes) in Myosin Binding Protein (MYBPC3; implicated in cardiac hypertrophic myopathy) gene to be associated with endurance athlete status (P=1.43E-08, odd ratio 2.2). Homozygotes carriers of rs1052373 G allele in Russian athletes had significantly greater VO2max than carriers of the AA+AG (P = 0.005). Subsequent metabolomics analysis revealed several amino acids and lipids associated with rs1052373 G allele (1.82x10-05) including the testosterone precursor androstenediol (3beta, 17beta) disulfate. Conclusion: This is the first report of genome-wide significant SNP and related metabolites associated with elite athlete status. Further investigations of the functional relevance of the identified SNPs and metabolites in relation to enhanced athletic performance are warranted.